Batch-Process Video Watermarks in Blender
I use Blender, Imagemagick and FFMPEG for this kind of work. Command line FFMPEG is much faster and straight forward tool for your job, although a linux blender command line would likely compare in speed, but might be more complex to implement.

However, you will have a lot more support with FFMPEG for this kind of common work, and the command line is simple (inputs, overlay location, output):

ffmpeg -i input-video.mp4 -i watermark.png -filter_complex "overlay=0:0" watermarked-video-output.mp4

Which would be easily looped in linux to operate on a batch of videos.